updating bash wrappers

runSnakes.sh

@@ -4,26 +4,25 @@ echo "Launching snakemake workflow..."
 sleep 3
 echo "Beginning executing on: $(date)"
 
-source activate snakemake
-
-echo "Demultiplexing SQ libraries"
+#echo "Demultiplexing SQ libraries"
 #snakemake --profile config/slurm --snakefile workflow/demux.smk
-echo "Demultiplexing completed"
+#echo "Demultiplexing completed"
 
 echo "Preparing fastq for profiling."
 
-echo "Collecting SQ runs: $(ls results/SQ*).."
-
-
-# snakemake --profile config/slurm --snakefile workflow/prepare.smk
-# echo "Preparations completed."
+echo "Collecting SQ runs: $(ls -r results | grep SQ)"
 
-# echo "Starting profiling..."
-# snakemake --profile config/slurm --snakefile workflow/profile.smk
-# echo "profiling completed."
+for i in $(ls -r results | grep SQ); 
+do
+	echo $i;
+
+	snakemake --profile config/slurm_profiles/eRI --config LIBRARY=$i --snakefile workflow/GBS-TaFFE.smk results/$i/00_QC/seqkit.report.KDR.txt &&
+
+	snakemake --profile config/slurm_profiles/eRI --config LIBRARY=$i --snakefile workflow/Ref-Free.smk &&
+
+	ln -s /scratch/2023-mbie-rumen-gbs/GBS-TaFFE/results/$i /projects/2024-gbs_microbiomes_processing/Pipeline/ 
 
-##snakemake --rulegraph | dot -T svg > rulegraph.svg
+done
 
-conda deactivate
 
 echo "snakemake run completed: $(date)"

runSnakes_GBS-TaFFE.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+### Wrapper script for launching snakemake workflows ###
+echo "Launching snakemake workflow..."
+sleep 3
+echo "Beginning executing on: $(date)"
+
+#echo "Demultiplexing SQ libraries"
+#snakemake --profile config/slurm --snakefile workflow/demux.smk
+#echo "Demultiplexing completed"
+
+echo "Preparing fastq for profiling."
+
+echo "Collecting SQ runs: $(ls -r results | grep SQ)"
+
+for i in $(ls -r results | grep SQ); 
+do
+	echo $i;
+
+	snakemake --profile config/slurm_profiles/eRI --config LIBRARY=$i --snakefile workflow/GBS-TaFFE.smk
+
+done
+
+
+echo "snakemake run completed: $(date)"